Uni-hemispheric concurrent dual-site anodal transcranial direct current stimulation (UHCDS a-tDCS) of the primary motor cortex (M) and the dorsolateral prefrontal cortex (DLPFC) may enhance the efficacy of a-tDCS after stroke. However, the cellular and molecular mechanisms underlying its beneficial effects have not been defined. We aimed to investigate the effect of a-tDCS on brain metabolite concentrations (N-acetyl aspartate (NAA), choline (Cho)) in stroke patients using magnetic resonance spectroscopy (MRS). In this double-blind, sham-controlled, randomized clinical trial (RCT), 18 patients with a first chronic stroke in the territory of the middle cerebral artery trunk were recruited. Patients were allocated to one of the following two groups: (1) Experimental 1, who received five consecutive sessions of a-tDCS M (active)-DLPFC (active). (2) Experimental 2, who received five consecutive sessions of a-tDCS M1 (active)-DLPFC (sham). MRS assessments were performed before and 24 h after the last intervention. Results showed that after five sessions of a-tDCS there were no significant changes in NAA and Cho levels between groups (Cohen's d = 1.4, Cohen's d = 0.93). Thus, dual site a-tDCS did not affect brain metabolites compared to single site a-tDCS M.